rs76878398
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_025193.4(HSD3B7):c.856G>A(p.Ala286Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,314 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_025193.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD3B7 | NM_025193.4 | c.856G>A | p.Ala286Thr | missense_variant | 7/7 | ENST00000297679.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD3B7 | ENST00000297679.10 | c.856G>A | p.Ala286Thr | missense_variant | 7/7 | 1 | NM_025193.4 | P1 | |
ENST00000624286.1 | n.342C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
HSD3B7 | ENST00000262520.10 | c.*102G>A | 3_prime_UTR_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00719 AC: 1095AN: 152212Hom.: 8 Cov.: 34
GnomAD3 exomes AF: 0.00169 AC: 422AN: 249966Hom.: 3 AF XY: 0.00124 AC XY: 168AN XY: 135382
GnomAD4 exome AF: 0.000791 AC: 1156AN: 1460984Hom.: 15 Cov.: 65 AF XY: 0.000660 AC XY: 480AN XY: 726862
GnomAD4 genome ? AF: 0.00719 AC: 1096AN: 152330Hom.: 8 Cov.: 34 AF XY: 0.00715 AC XY: 533AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at